Nucleic Acid Purification

ABSTRACT

The inventive self-contained apparatus for isolating nucleic acid, cell lysates and cell suspensions from unprocessed samples apparatus, to be used with an instrument, comprises at least one input, and: (i) a macrofluidic component, comprising a chamber for receiving said unprocessed sample from a collection device and at least one filled liquid purification reagent storage reservoir; and (ii) a microfluidic component in communication with said macrofluidic component via at least one microfluidic element, said microfluidic component further comprising at least one nucleic acid purification matrix; and (iii) a drive mechanism on said instrument for driving said liquid purification reagent, through said microfluidic element and said nucleic acid purification matrix, wherein the only inputs to said apparatus are via said chamber and said drive mechanism.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.12/699,564, filed Feb. 3, 2010, and claims the benefit of the filingdates of U.S. Provisional Application Ser. No. 61/206,690, filed Feb. 3,2009; and No. 61/207,017, filed Feb. 6, 2009. Each of the preceding arehereby incorporated by reference in their entirety.

BACKGROUND OF THE INVENTION

A. The Unmet Need—Unprocessed Clinical and Forensic Samples

From the first isolation of nucleic acids by Miescher and Altmann in thesecond half of the nineteenth century (Miescher, Friedrich (1871) “Ueberdie chemische Zusammensetzung der Eiterzellen,” in F. Miescher. DieHistochemischen and physiologischen Arbeiten Vol. 2:3-23) to the mostsophisticated molecular biological techniques available today, theprocess of DNA extraction has been streamlined substantially.Nevertheless, there is a pressing need in the clinical, biothreatdetection, and forensics communities for sensitive, robust, and reliableintegrated methods of DNA purification that are rapid, cost-effective,and neither labor- nor space-intensive. In particular, there is an unmetneed for methods and devices that can rapidly purify nucleic acids fromunprocessed clinical or forensic field samples without any manualhandling or processing.

Ideally, novel methods for nucleic acid purification are needed toaddress the numerous and varied existing and emerging markets fordelivering genomic information, particularly the delivery of genomicinformation in the field, and for point-of-care and near point-of-careapplications. For example, in the field of human identification, thereis an unmet need in the forensic community to be able to generate a DNAfingerprint rapidly, whether in the laboratory or in the field (e.g. atborders, ports of entry, the battlefield, and military checkpoints).

Similarly, in order to protect civilian and military populations, it iscritical to improve the identification of environmental biothreats. Morerapid, more sensitive, more specific, and more detailed identificationwill allow improved strategic and tactical responses by civilian andmilitary authorities, and more effective remediation activities. Therapid application of nucleic acid analysis technologies includingnucleic acid amplification, hybridization, and sequencing can providecritical information in this regard.

Furthermore, the ability to rapidly diagnose clinical infections(whether caused by biothreats or conventional pathogens) would have aprofound impact on society. For example, drawing a blood sample from aseptic patient and determining both the identity of the pathogen orpathogens as well as their antibiotic resistance profiles based onnucleic acid analyses within an hour or less would allow specificantimicrobial therapy to begin immediately (the analogous situation forviral diagnostics and drug resistance profiles is also criticallyimportant). The ability to rapidly generate nucleic acid analyticinformation from clinical samples would also have substantial impact onthe diagnosis and treatment of a wide range of diseases ranging fromcancers to immune system disorders; essentially every category ofdiseases would be impacted. The same approach could also be applied topharmacogenomics, the use of genetic information to predict thesuitability of a given pharmacologic intervention.

B. Prior Art Approaches to DNA Purification

The basic approach to extraction and purification of nuclear DNA frommammalian cells was developed over three decades ago (N. Blin, D. W.Stafford (1976). A general method for isolation of high molecular weightDNA from eukaryotes. Nucleic Acids Res. 3(9): 2303-8) and has two majorsteps: the lysis of the cell types of interest and the purification ofDNA from other cellular components in solution (particularly proteins)and cellular and tissue debris. Cell lysis and (when appropriate) DNAsolubilization can be accomplished by mechanical (reviewed in J. Brent(1998). Breaking Up Isn't Hard To Do: A cacophony of sonicators, cellbombs and grinders” The Scientist 12(22):23) and non-mechanicaltechniques. Simple mechanical approaches include the use of a blendersand homogenization by forcing cells through restrictive openings.Sonication is based on the exposure of cells to high-frequency soundwaves, and bead approaches are based on exposing cells to violent mixingin the presence of various beads.

Chemical disruption of cells is an alternative to mechanical disruption.Detergents are important chemical lytic agents that act by disruptinglipid bilayers. Additional properties of detergents may allow proteinstructure to be maintained (e.g. zwitterionic and nonionic detergents)or disrupted (ionic detergents). Sodium dodecyl sulfate (SDS), an ionicdetergent, is commonly used in forensic DNA extraction protocols due inpart to its ability to solubilize macromolecules and denature proteinswithin the cell (J. L. Haines et al (2005) Current Protocols in HumanGenetics Vol. 2, (2005 John Wiley and Sons, Inc. Pub.). Proteinase K isoften used in tandem with detergent-based (e.g. SDS, Tween-20, TritonX-100) lysis protocols. Another form of detergent lysis is based on FTApaper (L. A. Burgoyne (1997) Convenient DNA Collection and Processing:Disposable Toothbrushes and FTA Paper as a Non-threatening Buccal-CellCollection Kit Compatible with Automatable DNA Processing, 8thInternational Symposium on Human Identification, Sep. 17-20, 1997Orlando, Fla.; G. M. Fomovskaia et al., U.S. Pat. No. 6,958,392). Thisis a cellulose filter impregnated with a weak base, an anionicdetergent, a chelating agent, and preservatives.

In the case of a clinical or environmental sample, a critical first steptowards nucleic acid analysis is the isolation or purification of someor all of the nucleic acid present in the sample. The biologicalmaterial in the sample may be lysed and nucleic acids within the lysatemay be purified prior to further analysis. Alternatively, nucleic acidscontained within the lysate may be analyzed directly (e.g. Phusion BloodDirect PCR kit (Finnzymes, Espoo, FN) and Daniel et al., U.S. Pat. No.7,547,510).

As those skilled in the art will recognize, purifying nucleic acids fromunprocessed clinical, environmental, or forensic samples requires theautomation of pre-processing steps suited to the particular field sampleunder investigation. The diversity of sample types, sample volumes,sampling technologies, sample collection devices, sample processingrequirements, and the complexities inherent in resolving field sampleshas created an unmet need for robust methods and devices for purifyingnucleic acids from such diverse samples.

C. Microfluidic Approaches to Purification from Clinical andEnvironmental Samples

The field of microfluidics offers a potential solution to the unmet needfor methods and devices capable of isolating nucleic acids fromunprocessed clinical, environmental, and forensic samples. Microfluidicsis based on the manipulation of small fluid volumes of microliters orless and emerged as a hybrid of molecular biology and microelectronicsin the early 1990's (See Manz et al. Sens. Actuators B1:244-248 (1990)).A major focus in microfluidics is to integrate multiple components todevelop a system with sample-in, results-out functionality (reviewed inErickson et al., Anal. Chimica Acta 507: 11-26 (2004)).

Some progress using this approach has been made with regard toenvironmental detection of biothreats. The automated pathogen detectionsystem (Hindon et al., Anal. Chem. 77:284-289 (2005)) collects airsamples and performs microfluidic DNA extraction and real-time PCRcapable of detecting B. anthracis and Y. pestis (detection limits werebetween 10³-10 ⁷ organisms per mL of concentrated sample). The Cepheid(Sunnyvale, Calif.) GeneXpert system also collects air samples andperforms integrated B. anthracis spore lysis (by microsonication), DNAextraction, and real-time PCR (detection limits were 68 cfu (equivalentto 148 spores) per mL concentrated sample for Ames spores and 10²-10 ³cfu per mL concentrated sample for Sterne spores). Despite theseadvances, there is no available system or device capable of purifyingunprocessed nucleic acids from clinical or environmental samples (orfrom environmental samples collected manually) without humanintervention. Indeed, all of the available technologies rely on manualprocessing of some or all of the steps.

D. DNA Purification from Forensic Samples

One of the earliest DNA purification methods for forensic samples wasthe use of phenol/chloroform extraction (D. M. Wallace (1987) Large andsmall scale phenol extractions. Methods Enzymol. 152:33-41; Maniatis, T.et al., “Purification of Nucleic Acids” in Molecular Cloning: ALaboratory Manual, 3rd Ed. Cold Spring Harbor Laboratory, Cold SpringHarbor, N.Y.). In this method, most protein moves to the organic phaseor the organic-aqueous interface, and solubilized DNA remains in theaqueous phase. The DNA-containing phase can be subjected to ethanolprecipitation, and DNA isolated following a series of centrifugation andwash steps. In forensic practice, DNA is often recovered from theaqueous phase with centrifugal dialysis devices, such as the Microconcolumns (Millipore Corporation, Billerica, Mass.). The advantage of theorganic extraction approach is that it yields high quality DNApreparations (with relatively low amounts of protein and relatively lowdegradation) and remains one of the most reliable methods availabletoday. The major disadvantages are that the procedure is time- andlabor-intensive, requires cumbersome equipment, and is relativelydifficult to adapt to high-throughput settings.

Accordingly, the forensic community has moved to a series ofpurification technologies that are simpler to use, many of which serveas the basis of commercially available kits. There are an enormousnumber of approaches to nucleic acid purification, several of which aresummarized as follows:

Silica matrices/chaotropic agents. The use of silica beads for DNAisolation has been a standard technique for over a quarter century, withthe initial protocols based on the binding of DNA to silica in thepresence of chaotropic agents such as sodium iodide (B. Vogelstein etal., (1979) “Preparative and analytical purification of DNA fromagarose,” Proc Nat Acad Sci USA 76(2):615-9). Many years earlier,guanidinium salts had been found to be potent destabilizers ofmacromolecules (von Hippel P. H. et al., (1964) “Neutral Salts: TheGenerality of Their Effects on the Stability of MacromolecularConformations.” Science 145:577-580). Certain guanidinium salts alsohave the advantage of deactivating nucleases (Chirgwin J. M. et al.,(1979) “Isolation of biologically active ribonucleic acid from sourcesenriched in ribonuclease,” Biochemistry 18(24):5294-9). Theseobservations were synthesized by Boom (Boom, R. et al., (1990) “Rapidand Simple method for purification of nucleic acids,” J Clin Microbiol.28(3):495-503), who, in effect, used two related properties ofguanidinium salts. The first, the ability of the salts to lyse cells,and the second, the ability of the salts to enhance DNA binding tosilica particles, have led to a number of lysis/purification approacheswidely utilized in forensics laboratories today (e.g. DNAIQ Systems,Promega, Madison, Wis.). An alternative to silica beads is the use ofsilica membranes (QIAamp, Qiagen Hilden, Del.). In addition, the silicabeads themselves may be modified to further enhance DNA binding.

Silica matrices/non-chaotropic agents. Silica matrices can also beutilized in the absence of chaotropes. One approach is to modify silicabeads such that they have a net positive charge at a given pH and arecapable of binding DNA (Baker, M. J., U.S. Pat. No. 6,914,137). Themodification contains an ionizable group, such that the DNA binding isreversed at a higher pH (when the ionizable group is neutral ornegatively charged), sometimes at elevated temperature. As wide swingsin pH can damage DNA, a critical feature of this approach is to choose amodification that allows reversible binding of DNA within a relativelynarrow pH range. A widely used approach of this type is based on theChargeSwitch bead (Life Technologies, Inc. Carlsbad, Calif.).

Magnetic Beads. Although DNA binding properties are determined primarilyby the surface structure of a given bead, the use of magnetic beads hasbecome increasingly important in DNA purification protocols. Theseparticles are generally paramagnetic; they are not themselves magneticbut form dipoles when exposed to a magnetic field. The utility of thesebeads relates to their ease of handling and adaptation to automatedsystems. For example, beads can be readily removed from a suspension inthe presence of a magnet, allowing them to be washed and transportedefficiently. Two commonly used magnetic beads are the ChargeSwitch andDNAIQ beads described above.

Ion exchange. Ion exchange allows DNA molecules to reversibly bind to animmobile bead. The bead generally consists of a porous organic orinorganic polymer with charged sites that allow one ion to be replacedby another at a given ionic strength. In practice, a solution containingDNA and other macromolecules is exposed to the ion exchange resin. Thenegatively charged DNA (due to its phosphate backbone) binds relativelystrongly to the resin at a given salt concentration or pH. Protein,carbohydrate, and other impurities bind relatively weakly (if at all)and are washed from the beads (e.g. in a column format or bycentrifugation). Purified DNA can then be eluted in a high ionicstrength buffer. A commercially available anion exchange resin usedtoday is based on DEAE-modified silica beads (Genomic-tip, Qiagen).

Chelex. Chelex-100 (Bio-Rad, Hercules, Calif.). is a modified resin thatefficiently binds multivalent metal cations. As such cations arerequired for enzymes that degrade DNA and themselves inhibit PCRenzymes, this method is representative of those that essentially avoid aDNA purification step (Walsh P. S. et al., Chelex 100 as a medium forsimple extraction of DNA for PCR-based typing from forensic material.Biotechniques 10(4):506-13).

When using cotton swabs to collect material, there can be problemsremoving biological material from the cotton matrix; as the cotton swabdries after collection, the biological material can adhere to the swab.For example, due to the saccharic composition of the spermatocytemembrane, spermatocytes stick to solid supports, especially cotton(Lazzarino, M. F. et al, (2008) DNA Recovery from Semen Swabs with theDNA IQ System. Forensic Science Communications 10(1)). In order torelease the maximum amount of material from the swabs, a variety ofbuffers have been tested and compared to the standard differentialextraction buffer. Use of detergents such as 1-2% sodium dodecyl sulfate(SDS) has shown to increase sperm cell recovery (Norris, J. V. et al.,(2007) “Expedited, chemically enhanced sperm cell recovery from cottonswabs for rape kit analysis.” J Forensic Sci 52(4): 800-5). Also, theaddition of low amounts of cellulase has shown to release moreepithelial and sperm cells from the cotton swab matrix than bufferelution alone (Voorhees, J. C. et al., (2006). “Enhanced elution ofsperm from cotton swabs via enzymatic digestion for rape kit analysis.”J Forensic Sci 51(3): 574-9).

There can be many challenges to obtaining forensic short tandem repeat(STR) profiles from biological materials including low quantity orquality of DNA. Low copy number samples (containing less than 50-100picograms of DNA) as well as low quality, degraded samples requirehighly efficient collection, extraction, and amplification procedures.These samples are seen in a variety of forensic evidence including touchevidence and aged samples. Amplification kits such as the LifeTechnologies Minifiler™ have smaller amplicon sizes which have shown toincrease the ability to obtain STR profiles from these difficultsamples.

PCR inhibitors are another challenge and must be eliminated beforedownstream applications can be performed. Common inhibitors are indigodyes from denim, heme from blood, humic acid found in plants and soil,and collagen found in various tissues. The majority of these inhibitorsare effectively eliminated using silica based DNA extraction methods oradditional purification with charge or size exclusion columns. Thepresence of inhibitors can be detected by performing PCR with internalpositive controls. If present, some inhibitors can be neutralized byvarious treatments including sodium hydroxide washes or furtherpurification with Millipore Microcon YM® columns.

The need to reconcile the “real world” requirements of sample collectionwith the microfluidic requirements of a fully integrated microfluidicDNA processing biochip can be referred to as the “macro-to-microinterface” or the “world-to-chip interface” (Fredrickson, C. and Fan, Z.(2004) “Macro-to-micro interfaces for microfluidic devices,” Lab Chip4(6): 526-33). Much of the reported research on addressing thisinterface is focused on resolving the mismatch between the macrofluidicand microfluidic volumetric requirements, but little or no researchconcerning the reconciling of specific forensic sampling requirementsand formats with microfluidic devices has been reported.

The (non-forensic) volumetric mismatch has been commercially addressedby Agilent (Santa Clara, Calif.) in the Bioanalyzer 2100 by the use of acapillary to aspirate samples from a microtiter plate to a chip forenzyme assays (Lin 2003). Similarly, Gyros (Uppsala, SE) has developed acapillary dispenser for a LabCD system where samples are aspirated froma well plate into a dispensing nozzle and then directed upwards onto arotating device (Jesson 2003). These devices, however, do not addressthe format incompatibility of collected forensic samples—particularly onthe commonly used collection devices based on swabs.

E. Partially Automated DNA Purification

A variety of laboratory instruments have been developed for thepartially automated purification of nucleic acids. For example, theMaxwell 16 instrument (Promega) is designed to purify nucleic acids fromforensic samples. To purify DNA from a buccal swab, the operatorperforms a number of steps including cutting the cotton collectionportion in half, placing it into a 1.5 mL centrifuge tube, preparing andadding lysis reagents, incubating the sample in a heat block, vortexingthe tube, transferring the reagents and swab sample to a spin basket,and centrifuging the basket. Next, a plunger is placed into the Maxwellcartridge, the sample is pipetted into the cartridge, and the cartridgeis placed into the instrument for nucleic acid purification.

The iPrep instrument (Life Technologies) is also used for the processingof forensic and clinical samples to purify nucleic acids. For example,the tip of a buccal swab is placed into a 1.5 mL centrifuge tube andsubjected to a series of manual steps similar to those required for theMaxwell 16. After manual sample preparation, the crude lysate istransferred to a 1 mL elution tube for processing within the instrument.The Qiagen EZ1, BioRobot M48, and Qiacube systems (Qiagen) partiallyautomate nucleic acid purification. Buccal swabs are collected, allowedto dry for two hours, and manually processed essentially as with theinstruments described above. Innuprep (analytikJena, Itzehoe, Del.),LabTurbo (Taigen, Taipei, T W), Xiril 150 (Xiril A G, Hombrechtikon, CH), and Quickgene (FujiFilm Corp., Tokyo, JP) systems are partiallyautomated instruments requiring substantial user manipulation andintervention. U.S. Patent App. Pub. No. 20080003564 (Chen et al)describes a macrofluidic sample processing tube that accepts a swab andtransports reagents mechanically using macrofluidic features andflexible tubing. US Patent App. Pub. No. 20070092901 (Ligler, F. et al.)have described a system that accepts liquid biological samples forsemi-automated nucleic acid purification.

Several groups including those of Landers (Wolfe, K. A. et al., (2002)Toward a microchip-based solid phase extraction method for isolation ofnucleic acids. Electrophoresis 23 (5):727-33; Wen, J. et al., (2006) DNAextraction using a tetramethyl orthosilicate-grafted photopolymerizedmonolithic solid phase. Anal Chem. 78(5):1673-81; Easley, C. J. et al.,(2006) A fully integrated microfluidic genetic analysis system withsample-in-answer-out capability. Proc Natl Acad Sci USA103(51):19272-7); Hagan K. A. et al. (2008) Microchip-based solid-phasepurification of RNA from biological samples, Anal Chem 80:8453-60),Locascio (Becker, H. et al., (2002) Polymer microfluidic devices Talanta56(2):267-287; Martynova, L. et al., (1997) Fabrication of plasticmicrofluid channels by imprinting methods. Anal Chem. 69(23):4783-9),Mathies (Lagally, E. T. et al., (2001) Fully integrated PCR-capillaryelectrophoresis microsystem for DNA analysis. Lab Chip 1(2):102-7:Yeung, S. H., et al., (2006) Rapid and high-throughput forensic shorttandem repeat typing using a 96-lane microfabricated capillary arrayelectrophoresis microdevice. J Forensics Sci. 51(4):740-7), and others(Liu R. H. et al., (2004) “Self-contained, fully integrated biochip forsample preparation, polymerase chain reaction, amplification, and DNAmicroarray detection Anal Chem 76(7):1824-31) have been working onmicrofluidics for DNA purification and analysis (reviewed in Liu, P. andMathies, R. A., (2009), “Integrated microfluidic systems forhigh-performance genetic analysis.” Trends in Biotechnology27(10):572-81). Easley has demonstrated DNA isolation from 750nanoliters of whole blood and 1 microliter of nasal aspirate using aguanidinium lysis/silica bead purification protocol (Easley, C. J. etal., Proc Natl Acad Sci supra). The whole blood sample containedapproximately 2.5 million bacteria (Bacillus anthracis) per mL 1500-2000cfu in the 750 mL sample), a concentration too high to be relevant forclinical diagnostics. U.S. Patent App. US2008/0014576 A1 describesnucleic acid purification modules that accept samples for purificationin solutions, beads, colloids, or multiple-phase solutions and may beintegrated with downstream preparation devices such as thermal cyclersand separation instruments.

SUMMARY OF THE INVENTION

The inventions of this disclosure comprise apparatus, methods andinstruments for isolating nucleic acid, cell lysates and cellsuspensions from unprocessed samples. In one invention, the apparatuscomprises a self-contained apparatus for isolating nucleic acid from anunprocessed sample, said apparatus to be used with an instrument, saidapparatus comprising, at least one input, and:

(i) a macrofluidic component, comprising a chamber for receiving saidunprocessed sample from a collection device and at least one filledliquid purification reagent storage reservoir; and

(ii) a microfluidic component in communication with said macrofluidiccomponent via at least one microfluidic element, said microfluidiccomponent further comprising;

-   -   at least one nucleic acid purification matrix

(iii) a drive mechanism on said instrument for driving said liquidpurification reagent, through said microfluidic element and said nucleicacid purification matrix, wherein the only inputs to said apparatus arevia said chamber and said drive mechanism.

In another invention, the apparatus comprises a self-contained apparatusfor isolating nucleic acid from an unprocessed sample, said apparatus tobe used with an instrument, said apparatus comprising, at least oneinput, and:

(i) a macrofluidic component comprising:

-   -   a chamber for receiving said unprocessed sample from a        collection device;    -   at least two pre-filled lysis reagent storage reservoirs;    -   a pre-filled wash reagent storage reservoir; and    -   a pre-filled elution reagent storage reservoir; and

(ii) a microfluidic component in communication with said macrofluidiccomponent via at least one microfluidic element, said microfluidiccomponent further comprising; at least one nucleic acid purificationmatrix;

(iii) a drive mechanism on said instrument for driving said first andsecond lysis reagents, said wash reagent, and said elution reagent andsequentially through said microfluidic element and said nucleic acidpurification matrix, wherein the only inputs to said apparatus are viasaid chamber and said drive mechanism.

In related inventions, the claimed apparatus may have collection devicesand/or chambers are labeled, said labels comprising and a bar code orRFID. In other related inventions, the drive mechanisms may bepneumatic, mechanical, magnetic, or fluidic. In still other relatedinventions the unprocessed sample comprises: (i) a nasal swab,nasopharyngeal swab, buccal swab, oral fluid swab, stool swab, tonsilswab, vaginal swab, cervical swab, blood swab, wound swab, or tubecontaining blood, sputum, purulent material, or aspirates; (ii) aforensic swab, cutting, adhesive tape lift, or card; or (iii) anenvironmental air filter, water filter, or swab.

In other related inventions the purification matrix of the claimedapparatus comprises silica membranes, silica beads, silica magneticbeads, ion exchange resins, or ion exchange beads. In still otherrelated inventions the microfluidic component of the claimed apparatuscomprises channels, reservoirs, active valves, passive valves,pneumatically actuated valves, reaction chambers, mixing chambers,venting elements, access holes, pumps, metering elements, mixingelements, heating elements, magnetic elements, reaction chambers,filtration elements, purification elements, drive lines, and actuationlines.

Another invention of this disclosure is a method for purifying nucleicacids from an unprocessed sample comprising,

providing a sample comprising nucleic acids to the chamber of a claimedapparatus;

driving at least a portion of a first lysis reagent from said firstlysis reagent chamber into the chamber to provide a first mixture;

driving at least a portion of a second lysis reagent from said secondlysis reagent chamber into the chamber to provide a second mixture;

driving at least a portion of the said second mixture through thepurification membrane to provide a filtrate and a retentate, wherein theretentate comprises at least a portion of the nucleic acids;

driving at least a portion of the wash reagent through the purificationmembrane to provide a washed retentate and a waste;

optionally drying the washed retentate; and

collecting at least a portion of the nucleic acids from the washedretentate by driving at least a portion of an elution reagent from theelution reagent chamber through the purification matrix.

Yet another invention of this disclosure is a method for purifyingnucleic acids from an unprocessed sample comprising,

providing a sample comprising nucleic acids to the chamber of a claimedapparatus;

driving at least a portion of a first lysis reagent from said firstlysis reagent chamber into the chamber to provide a first mixture;

bubbling a gas through the first mixture to provide a stirred firstmixture

driving at least a portion of a second lysis reagent from said secondlysis reagent chamber into the chamber to provide a second mixture; and

driving at least a portion of the stirred first mixture through thepurification matrix to provide a filtrate and a retentate, wherein theretentate comprises at least a portion of the nucleic acids;

driving at least a portion of the wash reagent through the purificationmatrix to provide a washed retentate and a waste;

optionally drying the washed retentate;

driving at least a portion of an elution reagent from the elutionreagent chamber through the purification matrix to provide an elutednucleic acid solution; and bubbling a gas through the eluted nucleicacid solution to provide a homogenized eluted nucleic acid solution.

Still another invention of this disclosure is a method for purifyingnucleic acids from pathogens in whole blood comprising,

providing a sample comprising anticoagulated whole blood and pathogensin a blood collection tube to the sample collection chamber of a claimedapparatus;

driving at least a portion of the blood through a leukocyte retentionfilter to provide a reduced-leukocyte filtrate;

driving at least a portion of a leukocyte wash reagent through theleukocyte retention filter to provide a washed reduced-leukocytefiltrate;

driving at least a portion of the a reduced-leukocyte filtrate through apathogen capture membrane

driving at least a portion of the pathogen resuspension solution acrossthe capture membrane to provide a concentrated pathogen suspension

driving at least a portion of the concentrated pathogen suspension intoa first lysis reagent chamber containing said first lysis reagent toprovide a first mixture;

driving at least a portion of a second lysis reagent from said secondlysis reagent chamber into the first lysate reagent chamber to provide asecond mixture; driving at least a portion of the said second mixturethrough the purification membrane to provide a filtrate and a retentate,wherein the retentate comprises at least a portion of the nucleic acids;

driving at least a portion of the wash reagent through the purificationmembrane to provide a washed retentate and a waste;

optionally drying the washed retentate; and

collecting at least a portion of the nucleic acids from the washedretentate by driving at least a portion of an elution reagent from theelution reagent chamber through the purification matrix.

Another invention of this disclosure is a method for purifying nucleicacids from pathogens in whole blood comprising,

providing a sample comprising anticoagulated whole blood and pathogensin a blood collection tube to the sample collection chamber of a claimedapparatus;

driving at least a portion of the blood through a leukocyte retentionfilter to provide a reduced-leukocyte filtrate;

driving at least a portion of a leukocyte wash reagent through theleukocyte retention filter to provide a washed reduced-leukocytefiltrate;

driving at least a portion of the leukocyte resuspension solution acrossthe retention filter to provide a concentrated leukocyte suspension;

driving at least a portion of the concentrated leukocyte suspension intoa first lysis reagent chamber containing said first lysis reagent toprovide a first mixture;

driving at least a portion of a second lysis reagent from said secondlysis reagent chamber into the first lysate reagent chamber to provide asecond mixture; driving at least a portion of the said second mixturethrough the purification membrane to provide a filtrate and a retentate,wherein the retentate comprises at least a portion of the nucleic acids;

driving at least a portion of the wash reagent through the purificationmembrane to provide a washed retentate;

optionally drying the washed retentate; and

collecting at least a portion of the nucleic acids from the washedretentate by driving at least a portion of an elution reagent from theelution reagent chamber through the purification matrix.

In a related invention the method additionally comprises,

driving a leukocyte lysis solution into the concentrated leukocytesuspension to provide a differentially lysed suspension; driving atleast a portion of the differentially lysed suspension through apathogen retention filter; driving at least a portion of the retentionfilter wash reagent through the pathogen retention filter to provide awashed pathogen retentate; and resuspending, lysing, and purifyingnucleic acids from the pathogen retentate.

Another invention of this disclosure is a self-contained apparatus forgenerating cell lysate from an unprocessed sample, said apparatus to beused with an instrument, said apparatus comprising at least one input,and:

(i) a macrofluidic component, comprising: a chamber for receiving saidunprocessed sample from a collection device, and at least one filledreagent storage reservoir; and

(ii) a microfluidic component in communication with said macrofluidiccomponent via at least one microfluidic element; and

(iii) a drive mechanism on said instrument for driving said reagent,through said microfluidic element, wherein the only inputs to saidapparatus are via said chamber and said drive mechanism.

Yet another invention is a self-contained apparatus for lysing cellsfrom an unprocessed sample, said apparatus to be used with aninstrument, said apparatus comprising at least one input, and:

(i) a macrofluidic component, comprising a chamber for receiving saidunprocessed sample from a collection device and at least one pre-filledlysis storage reservoir; and

(ii) a microfluidic component in communication with said macrofluidiccomponent via at least one microfluidic element; and

(iii) a drive mechanism on said instrument for driving reagent in saidstorage reservoir, through said microfluidic element,

wherein the only inputs to said apparatus are via said chamber and saiddrive mechanism.

In a related inventive method for lysing cells from a sample comprisingusing the apparatus, comprising at least one input, and: providing asample comprising cells to a chamber; introducing said lysis reagentinto the chamber to provide a mixture; bubbling a gas through themixture to provide a stirred mixture; wherein the stirred mixturecomprises lysed cells.

Still another invention is a self-contained apparatus for generating asuspension of cells from an unprocessed sample, said apparatus to beused with an instrument, said apparatus comprising at least one input,and:

(i) a macrofluidic component, comprising: a chamber for receiving saidunprocessed sample from a collection device, and at least one filledreagent storage reservoir storing a substantially isotonic reagent; and

(ii) a microfluidic component in communication with said macrofluidiccomponent via at least one microfluidic element; and

(iii) a drive mechanism on said instrument for driving said reagent,through said microfluidic element, wherein the only inputs to saidapparatus are via said chamber and said drive mechanism.

In another invention, the instruments which comprise the claimedinventive apparatus also perform at least one of thermal cycling,capillary electrophoresis, microfluidic electrophoresis, nucleic acidfragment sizing, short tandem repeat (STR), Y-STR, and mini-STR, singlenucleotide polymorphism, PCR, highly multiplexed PCR, Real-time-PCR,Reverse Transcription PCR, sequencing, hybridization, microarray, VNTR,immunoassays, mass spectroscopy and RFLP analyses.

In still another invention, the apparatus of the invention can be placedinto or interface with another instrument that performs at least one ofthermal cycling, capillary electrophoresis, microfluidicelectrophoresis, nucleic acid fragment sizing, short tandem repeat(STR), Y-STR, and mini-STR, single nucleotide polymorphism, PCR, highlymultiplexed PCR, Real-time-PCR, Reverse Transcription PCR, sequencing,hybridization, microarray, VNTR, immunoassays, mass spectroscopy andRFLP analyses.

It also is an invention of this disclosure that the claimed apparatusand instruments are ruggedized to withstand transport and extremes of atleast one of temperature, humidity, and airborne particulates.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts an apparatus suitable for biothreat detection from ablood sample.

FIG. 2 is an electropherogram showing near-quantitative recovery of B.subtilis using a purification cartridge.

FIG. 3 is a side view of a purification cartridge for blood samples. Theblood collection tube is labeled 1, the cover is labeled 2; themacrofluidic component is labeled 3; the microfluidic component islabeled 4; a pneumatic interface port is labeled 5.

FIG. 4 is a side view of the macrofluidic component of a purificationcartridge for blood samples. The macrofluidic component is labeled 3;the first wash reservoir is labeled 6; the eluate homogenization chamberis labeled 7; the waste chamber is labeled 8; the eluate reservoir islabeled 9; the resuspension solution reservoir is labeled 10; the lysischamber is labeled 11; the ethanol reservoir is labeled 12; the lysisreservoir is labeled 13; the holding chamber is labeled 14; the secondwash reservoir is labeled 15 and the blood collection tube cavity islabeled 16.

FIG. 5 is a top view of the pneumatic layer of a purification cartridgefor blood samples. Pneumatic channels are labeled 17; through holes toreagent reservoirs and chambers of the macrofluidic component arelabeled 18 and pneumatic interface ports are labeled 19.

FIG. 6 is a top view of the microfluidic layer of a purificationcartridge for blood samples. Fluidic channels are labeled 20; the tracketch membrane is labeled 21; the Leukosorb filter is labeled 22 and thepurification filter is labeled 23.

FIG. 7 is a side view of a forensics cartridge. The swab cap is labeled24; the cover is labeled 25; the macrofluidic component is labeled 26;the microfluidic component is labeled 27 and the pneumatic interfaceports are labeled 28.

FIG. 8 is a side view of the macrofluidic component of a forensicscartridge. The macrofluidic component is labeled 26; the wash reservoiris labeled 29; the eluate homogenization chamber is labeled 30; theeluate reservoir is labeled 31; the swab chamber is labeled 32; theethanol reservoir is labeled 33; the lysis reservoir is labeled 34 andthe holding chamber is labeled 35.

FIG. 9 is a top view of the pneumatic layer of a forensics cartridge.Pneumatic channels are labeled 36; through holes to reagent reservoirsare labeled 37 and pneumatic interface ports are labeled 38.

FIG. 10 is a top view of the microfluidic component of a forensicscartridge. Fluidic channels are labeled 39; the particulate filter islabeled 40 and the purification filter is labeled 41.

FIG. 11 is an STR profile obtained from DNA purified from a buccal swab.

FIG. 12 is a STR profile obtained from DNA purified from a driedbloodstain sample.

FIG. 13 is an STR profile obtained from DNA purified from salivaisolated from saliva.

FIG. 14 is an STR profile obtained from DNA purified from a touchsample.

FIG. 15 is a side view of a cervical swab cartridge. The swab cap islabeled 42; the cover is labeled 43; the macrofluidic component islabeled 44; the microfluidic component is labeled 45 and a pneumaticinterface port are labeled 46.

FIG. 16 is a side view of the macrofluidic portion of a cervical swabcartridge. The wash reservoir is labeled 47; the eluate homogenizationchamber is labeled 48; the eluate reservoir is labeled 49; the swabchamber is labeled 50; the ethanol reservoir is labeled 51; the lysisreservoir is labeled 52; the holding chamber is labeled 53.

DETAILED DESCRIPTION OF THE INVENTION

The invention provides a series of apparatus, instrumentation, andmethods that can be used to provide rapid, efficient purification ofnucleic acids from a variety of biological sample types. As illustratedin the examples herein, nucleic acid can be purified based on devicescomprising both macrofluidic and microfluidic features and accompanyinginstrumentation. In general, the macrofluidic component of the apparatusof this invention comprises chambers (including sample, reagent storagereservoir, reaction, holding, homogenization, and waste chambers) withaggregate volume of 1-1000 mL or greater and individual volumes of 1 mLand greater. Particularly preferred are aggregate volumes in the rangeof 1-250 mL. The macrofluidic component may also optionally comprisechambers with volumes of 20-1000 μL. The microfluidic componentcomprises microfluidic elements with microliter and nanoliter volumes.It is preferred that the microfluidic elements have individual volumesin the range of 0.1-1000 μL and particularly preferred that theindividual elements have volumes of 0.1 to 100 μL.

The teachings of the invention can be applied to nucleic acidpurification such that the nucleic acid product can be removed andanalyzed separately or the nucleic acid can be transferred directly toanalytic modules in an integrated instrument. Types of analysis andapproaches to such integration include those described in Tan et al.,Integrated Nucleic Acid Analysis, PCT/US08/04462, which is herein fullyincorporated by reference.

The apparatus and instrumentation of the invention allow nucleic acid tobe purified from unprocessed biological samples. Unprocessed biologicalsamples are those that are collected by an individual and then insertedinto the sample receiving chamber of the apparatus with no intermediateprocessing steps (although the sample collection device may be labeledand/or stored prior to processing). The operator need only collect orotherwise obtain the sample, insert the sample into the apparatus,insert the apparatus into the instrument (not necessary if the apparatuswas previously placed in the instrument), and press a start button. Noprocessing, manipulation, or modification of the sample is requiredprior to insertion in the apparatus—the operator does not have to cut aswab, open a blood tube, collect a tissues or biologic fluid, transfer asample to another holder, or expose the sample to a reagent or acondition (e.g. heat, cold, vibration). Accordingly, the operator neednot have extensive training in the biological sciences or laboratorytechniques.

The apparatus of the invention are self-contained in that the onlyinputs to the apparatus are via the sample receiving chamber and thedrive mechanism. As all required reagents are present within theapparatus in pre-filled reagent storage reservoirs, the operator is notrequired to add process reagents to the apparatus. The fact that theapparatus contains all reagents on-board is an important factor in easeof operation. Similarly, as the instrument contains no purificationprocess reagents, the operator need not add reagents to the instrument.The self-contained nature of the apparatus minimizes operatingprocedures, maintenance procedures, and operator requirements. Takentogether, the self-contained apparatus and the use of unprocessedsamples dramatically simplifies the process of nucleic acidpurification. Another advantage of the self-contained apparatus of theinvention is that this format reduces both the possibility of samplecontamination as well as operator exposure to sample, reagents, andprocess waste.

Furthermore, the apparatus and instrumentation of the invention aredesigned to be operable outside of conventional laboratory environments.Depending upon the application, they can be ruggedized to withstandtransport and extremes of temperature, humidity, and airborneparticulates. Use of the invention by non-technical operators inoffices, out of doors, in the battlefield, in airports, at borders andports, and at the point-of-care will allow much broader application ofgenetic technology in society. The use of unprocessed samples in aself-contained apparatus further supports the broad application of themethods of the invention.

In practice, biological samples are collected using a myriad ofcollection devices, all of which can be used with the apparatus of theinvention. The collection devices will generally be commerciallyavailable but can also be specifically designed and manufactured for agiven application. For clinical samples, a variety of commercial swabtypes are available including nasal, nasopharyngeal, buccal, oral fluid,stool, tonsil, vaginal, cervical, and wound swabs. The dimensions andmaterials of the sample collection devices vary, and the devices maycontain specialized handles, caps, scores to facilitate and directbreakage, and collection matrices. Blood samples are collected in a widevariety of commercially available tubes of varying volumes, some ofwhich contain additives (including anticoagulants such as heparin,citrate, and EDTA), a vacuum to facilitate sample entry, a stopper tofacilitate needle insertion, and coverings to protect the operator fromexposure to the sample. Tissue and bodily fluids (e.g. sputum, purulentmaterial, aspirates) are also collected in tubes, generally distinctfrom blood tubes. These clinical sample collection devices are generallysent to sophisticated hospital or commercial clinical laboratories fortesting (although certain testing such as the evaluation ofthroat/tonsillar swabs for rapid streptococcal tests can be performed atthe point of care). Environmental samples may be present as filters orfilter cartridges (e.g. from air breathers, aerosols or water filtrationdevices), swabs, powders, or fluids.

Collection of biological evidence from crime scenes is a process thatgathers a number of cells from a variety of surfaces, preserves thecollected cells to minimize molecular degradation, and allows release ofthe collected material for downstream processing. Blood, semen,epithelial cells, urine, saliva, stool, various tissues, and bone can beassociated with the crime scene and require careful and effectivecollection (Lee, H. C. et al., (1998) “Forensic applications of DNAtyping: part 2: collection and preservation of DNA evidence.” Am JForensic Med Pathol 19(1): 10-8.

A common collection technique for forensic evidence is performed using acotton swab. A single swab is taken from an area or a wet-dry doubleswab technique can be used. The double swab technique may be the mostprevalent and a number of different fluids including water, bufferedsaline, or lysis buffers can be used to moisten the first swab (Leemans,P. 2006. “Evaluation and methodology for the isolation and analysis ofLCN-DNA before and after dactyloscopic enhancement of fingerprints.” IntCongress Ser 1288: 583-5). This technique allows for dried samples tobecome re-hydrated, with the majority of material collected on the firstswab and the dry second swab collecting the remainder of the sample. Inaddition to cotton, the swab collection matrix can be comprised ofvarious materials such as natural fiber (cotton) and synthetic matrices(modified cellulose, foam, Nylon, Polyester and Rayon). Swabs arecommercially available from Bode (Lorton, Va.), Puritan (Guilford, Me.),Fitzco (Spring Park, Minn.), Boca (Coral Springs, Fl.), Copan (Murrieta,Calif.) and Starplex (Etobicoke, ON, Canada). Swabbing can also beperformed using gauze-like materials, disposable brushes, orcommercially available biological sampling kits (Lauk, C. and Schaaf, J.2007. “A new approach for the extraction of DNA from postage stamps”Forensic Science Communications 9(1)).

Another forensic collection technique involves taking cuttings of thearea of interest such as a biological fluid from clothing; however thisdestroys the integrity of the evidence. Adhesive tape lifts are alsoused on a variety of surfaces to collect trace evidence that may containhuman DNA. Cards such as FTA cards (Whatman plc, Kent, UK) are also usedto collect samples.

Biological evidence from an individual that is present in person isoften collected using buccal swabs. A widely used commercial buccal swabis the SecurSwab (The Bode Technology Group, Lorton, Va.). Buccalsamples are collected by instructing the subject or operator to placethe swab into the mouth on the inner cheek surface and to move the swabup and down one or more times.

After the unprocessed samples of the invention are collected, if theyare not processed immediately they are sometimes allowed to dry toprevent fungal or bacterial growth. Evidentiary samples are generallynot immediately sealed in plastic, which can result in microbial growthand cause degradation of the DNA. Typically, swabs or cuttings areplaced in breathable containers made of paper or cardboard. Storingcollected evidence in cool, dry environments also minimizes sampledeterioration (Lee, H. C. and Ladd, C. (2001) “Preservation andCollection of Biological Evidence” Croat Med J 42(3): 225-8). To betruly useful to the forensic community, nucleic acid purificationapparatus, instrumentation, and methods should be able to obtain highlypurified nucleic acids from commercially available collection devicesand be compatible with accepted forensic collection and analysisprotocols.

Regardless of the type of sample, the sample receiving chamber of theapparatus and the cover (if present) are designed to accept and fitsnugly with the sample collection device. In the case of samples such ascloth or adhesive tape (e.g. sample collection devices that have nohandle or cap), following their placement into the chamber, asnug-fitting cap is placed on the cover to close the chamber. Dependingon application, the sample collection device can be locked (reversiblyor irreversibly) into the apparatus. Furthermore, the device andapparatus can form a seal (air- and water-tight); in this case, a ventor vent membrane may be placed to allow fluid flow into the chamber.Unless otherwise specified, the chambers of the apparatus that receivefluid from elsewhere on the apparatus must contain vents or ventmembranes to allow for air to escape during chamber filling.

The apparatus of the invention comprise a macrofluidic component and amicrofluidic component in communication with one another. Themacrofluidic component comprises a sample chamber for receiving abiological sample from a sample collection device, and other chambersthat may include reservoirs for purification reagents, holding chambers,homogenization chambers, metering chambers, reaction chambers, mixingchambers, and waste chambers. The microfluidic component comprises achamber comprising a nucleic acid purification media and at least onemicrofluidic feature and one pneumatic drive-line. The macrofluidicchambers are in communication with microfluidic features and themacrofluidic chambers are in communication with each other via themicrofluidic component. Fluids pass from one macrofluidic chamberthrough the microfluidic component back to another macrofluidic chamber.The volumes of the chambers are determined by the use of the purifiednucleic acids. For example, elution reservoir volume is chosen to allowthe final concentration of the purified nucleic acid to be optimal forsubsequent reactions.

Following the purification processes in the apparatus of the presentinvention, the nucleic acid solution provided may be transferred foradditional analytic steps. The nucleic acid solution may beautomatically transferred to other analytic modules within the sameinstrument, or the apparatus itself may be transferred to a compatibleinstrument. Alternatively, the chamber that collects the purifiednucleic acid sample may contain a removable nucleic acid storage tube.Samples processed according to this invention may be a precursor to awide variety of analytical methods, including without limitation nucleicacid fragment sizing, short tandem repeat (STR), Y-STR, and mini-STR,single nucleotide polymorphism, PCR, highly multiplexed PCR,Real-time-PCR, Reverse Transcription PCR, sequencing, hybridization,microarray, VNTR, and RFLP analyses. Similarly, the apparatus, methods,and instruments of the invention can also be applied to immunoassays andprotein and mass spectroscopy assays in general and other analyticalmethods well known to those skilled in the art.

The apparatus of the invention may also have an optional cover to routechannels between the drive mechanism of the instrument and each of theindividual chambers. In addition, the cover also provides optionalfunctions of venting gases within the chambers to the environment andlocking sample collection device following insertion. The covercomprises at least one layer, preferably fabricated of plastic.Additional layers can be added as the number of pneumatic channels orthe complexity of routing and other features increases. Layer featurescan be macrofluidic or microfluidic, and features can be fabricated byCNC machining, hot embossing patterns, die cutting, or laser cutting ofplastic sheets, or injection molding of thermoplastic resin. In additionthe incorporation of vent membranes into the layer can be achieved bywelding and bonding. When two or more layers are required, theindividual layers are bonded together to form a single part. Bondingmethods for fabrication of the cover include thermal bonding, solventbonding, ultrasonic bonding, adhesive and laser bonding.

The microfluidic component of the apparatus may contain a variety offine features or microfluidic elements, including channels (which may beindependent, connected, or networked), reservoirs, valves, reactionchambers, liquid and lyophilized reagent storage chambers, mixingchambers, mixing elements, venting elements, access holes, pumps,metering elements, heating elements, magnetic elements, reactionchambers, filtration elements, purification elements, drive lines,actuation lines, optical excitation and detection regions, opticalwindows. The microfluidic component of the apparatus may use valves forflow control to halt or allow flow of fluids within channels. Valves canbe passive or, most preferably, active, and valving approaches formicrofluidic devices are well known in the art (reviewed in Zhang, C.,et al. (2007) “Micropumps, microvalves, and micromixers within PCRmicrofluidic chips: Advances and trends.” Biotechnol Adv 25(5):483-514). Active valve structures include mechanical (thermopneumaticand shape memory alloy), non-mechanical (hydrogel, sol-gel, paraffin,and ice), and external (modular built-in, pneumatic, and non-pneumatic)microvalves. The pneumatic and mechanical microvalve structures can alsoapply either elastomeric or non-elastomeric membranes. Passive valvesinclude in-line polymerized gel, passive plug, and hydrophobic valves.

The fluids required for the methods of the invention are nucleic acidpurification reagents and gasses (e.g. air, nitrogen, or oxygen). Thepurification reagents and media can be based on any of thewell-characterized methods of the literature, including silicamatrices/chaotropic agents (Boom, R. et al., (1990), supra), silicamatrices/non-chaotropic agents, ion exchange, and many others as wellknown in the art. Many such methods are summarized in Current Protocolsin Molecular Biology (Edited by Ausubel et al, John Wiley and Sons,2010). Similarly, many types of purification media can be used in theapparatus. Silica nucleic acid binding membranes, for example, vary insize, pore size, flow rate, retention volume, reagent compatibility, andbinding capacity; appropriate membranes are chosen based on a givenapplication. Cell separation media are also selected based on thephysical and chemical properties of the cellular material to beseparated. Finally, in some cases, particle removal filters may be used,preferably to remove particulates that may inhibit, slow down, orotherwise interfere with a downstream separation or purificationprocess. In many forensic embodiments, particle removal filters arepreferred.

The drive mechanism to allow fluid transport throughout the apparatuscan be pneumatic, mechanical, magnetic, fluidic, or any other means thatallows precise control of the fluid movement. A pneumatic drive allowscontrolled flow or a controlled pressure or a controlled volumetricdisplacement of air (or other gasses) to the apparatus via one or moredrive lines, and are particularly preferred. The pneumatic drive linescan be utilized to move liquids, create bubbles, burst foils, actuatemechanical features, and perform any other movements required for agiven nucleic acid purification method. The drive of the instrument mustinterface with the drive lines of the apparatus. For a pneumatic drive,the interface may be located at one or more macrofluidic or microfluidicregions of the apparatus. The drive is contained within the instrument,which may also contain a power supply, a housing to accept theapparatus, features that allow ruggedization and protection fromenvironmental exposure, an on-board computer, a process controller, amonitor, and other features based on the nucleic acid analysis to beconducted. The pneumatic drive system may contain the followingcomponents: pumps, electromechanical valves, pressure regulators,pressure tanks, tubing, pneumatic manifolds, and flow and pressuresensors. The pneumatic drive system allows the generation and deliver ofa defined flow, pressure, or volume to each of the pneumatic lines ofthe apparatus. A process controller can execute a programmed scriptfollowing insertion of the unprocessed sample into the apparatus. Morethan one class of drive mechanism can be utilized with the apparatus.However, the use of a single drive mechanism, preferably pneumatic,reduces the complexity of both the instrument and the apparatus.

Once in the sample chamber, the biological sample may be lysed by anumber of methods. Chaotic bubbling is caused by the flow of fluid,preferably air, into a chamber of the macrofluidic component. The flowmay be turbulent, which may contribute shearing forces that wouldcontribute to cell lysis and which may be appropriate for mixing orhomogenization of reagents. Other approaches to potentiating lysisinclude mechanical actuation by vibration, ultrasonic actuation, andheat.

In one embodiment of the invention, the nucleic acid to be purified isDNA. Other embodiments are based on the purification of RNA and totalnucleic acids. The reagents required to purify DNA, RNA, and totalnucleic acids are well-known in the art. See, e.g., Gjerde, D. T. etal., RNA Purification & Analysis: Sample Preparation, Extraction,Chromatography (2009 Wiley-VCH Pub.); Ausubel, F. M. et al., (Eds).,Current Protocols in Molecular Biology (2008 John Wiley Pub.). Inanother embodiment of the invention, the apparatus contains macrofluidicand microfluidic elements that allow cell separation. These elements mayallow a variety of cell separations including white blood cells (WBC) tobe separated from red blood cells, bacteria or viruses to be separatedfrom host cells, sperm cells to be separated from vaginal epithelialcells, and intracellular viruses and bacteria to be separated from theirmammalian hosts.

The apparatus of the invention can be fabricated in several ways. Basedon the time and cost allotted for fabrication and the number ofapparatus to be fabricated a variety of methods are available. Theapparatus may be fabricated out of glass or more preferably, out ofthermoplastic polymers such as polyethylene, polypropylene,polycarbonate, polystyrene, cyclic olefin polymer, and cyclic olefincopolymer. The apparatus may be fabricated in one or more parts,macrofluidic and microfluidic. If the apparatus is made of plasticparts, the components may be bonded together using clamping, thermalbonding, ultrasonic bonding, solvent bonding, laser bonding, or adhesivebonding (bonding methods are reviewed in Tsao and DeVoe, MicrofluidNanofluid (2009) 6:1-16). A rapid and straightforward method offabrication is by computer-numerical-controlled machining. Other methodsinclude blow molding, extrusion, and embossing.

A preferred method of fabrication is by injection molding. Themacrofluidic portion of the apparatus of the invention comprises of aset of chambers of tubular structure that may be injection moldedtogether to form a single part. The top surfaces of each chamber arepreferably coupled pneumatically to a cover to provide pneumatic driveto each of the individual chambers. The bottom surfaces of each chamberare preferably coupled pneumatically and fluidically to the microfluidiccomponent. Tube-like structures that have been injection molded as asingle part include microtiter plates with 96, 384 and 1536 wells.Microcentrifuge plates with 96 wells in a 12×8 configuration 8.4 mm indiameter and 16 mm deep is described by Turner (U.S. Pat. No.6,340,589). While these plates have a high density of tubular structuresin high packing density, the depth of these tubes are not more 16 mm.PCR tubes-tube strips with 8 or 12 tubes have been fabricated in-line byinjection molding, with each tube being 8.65 mm in diameter and 30 mmdeep with a capability to hold 0.2 mL. These are all coupled versions ofthe plastic reaction vessel described by Gerken (U.S. Pat. No.4,713,219). These strip tubes have a low packing density, and areoriented in-line. Finally, injection molding of two long coupled tubesare described by Spehar (U.S. Pat. No. 4,753,536).

The tubular structures of the macrofluidic portion have thin walls. Wheninjection molded, the macrofluidic portion is essentially a series ofthin walled tubes held together as opposed to a solid block with tubesdrilled out. The tubes have wall thicknesses of 0.1-5.0 mm, preferably0.3 to 3.0 mm, more preferably 0.5 to 1.5 mm, still more preferably 0.7to 1.3 mm, and most preferably 0.9 to 1.2 mm.

The injection molded tubular structures of the macrofluidic portionpreferably have a tube length in excess of 16 mm, 18 mm, 20, mm, 25 mm,30 mm, 40 mm, 50 mm, 60 mm, 70 mm, 80 mm, 90 mm, or 100 mm. The tubularstructures are oriented in a two dimensional configuration. The tops ofthe tubular structures must be flat to achieve strong pneumatic couplingto optional cover, and the bottoms of the tubular structures must beflat to achieve strong pneumatic and fluidic coupling to themicrofluidic portion. Spacing of the tubular structures must bemaintained to accurately match the footprint of the microfluidicportion. The tubular structures may taper from top to bottom tofacilitate precise interfacing with the microfluidic component.Similarly, the form of the tubular structure may be adapted for aparticular purpose, such as a narrowed lower portion to facilitatechaotic bubbling and mixing or a narrowed central or upper portion tomaintain the position of a sample collection device.

The tubular structures of the macrofluidic component are packed densely,with one tube present per approximately 200 mm² surface area at the topof the component, more preferably approximately 150 mm². For otherapplications, one tube is present, preferably, per approximately 100 mm²surface area at the top of the component, and most preferably one tubeis present per approximately 50 mm² surface area at the top of thecomponent. Similarly, the surface area occupied by the tubularstructures as compared to the total area at the top of the macrofluidiccomponent is greater than 30%, more preferably greater than 40%. Forother applications, greater than 50%, for other applications still morepreferably greater than 60%, and most preferably greater than 90%.

The total volume of the apparatus is based in part on the number andvolume of chambers and the number of samples to be processedsimultaneously. The volume will be at least 2 mL, and may be 45 mL, 65mL, 100 mL, 500 mL, 1000 mL, 1500 mL or more, and preferably in therange of 45-1500 mL, and even more preferred in the range of 65-1500 mL.

The apparatus of the invention can accept and process one or moresamples. For some embodiments the apparatus may be configured to accept2, 4, 8, 16, 24, 36, 48, 96, 192, or 384 samples. As the number of unitsincreases, the approach to manufacturing may change. For example, asingle sample unit fabricated by injection molding may be used as thebasis for a 5-sample apparatus. Sets of 5-sample apparatus can bebonded, generating 10-sample, 15-sample apparatus. Alternatively, a15-sample apparatus can be manufactured as a single large unit. Theapparatus, instruments, and methods of the invention allow the rapidpurification of nucleic acids. From the time the process is initiatedfollowing insertion of the unprocessed sample to the time purifiednucleic acids from the sample are generated is preferably less than 30minutes, more preferably less than 20 minutes, even more preferably lessthan 10 minutes, and most preferably less than 5 minutes.

EXAMPLES Example I Extracellular Bacteria Present in Blood

Pathogens such as staphylococci, streptococci, and Yersiniaenterocolitica may be present in the blood. In some cases, it isadvantageous to isolate extracellular pathogens from the cellularelements of human (or other animal host) blood. For example, in order tomake best use of the advantages of a microfluidic device, an idealvolume for the purified DNA that is the end product of the DNAextraction/purification module is 25 μL or less. This volume can bequickly transferred and manipulated on a microfluidic chip. By limitingthis volume, however, an analogous limit is also placed on the maximumamount of DNA that can be present within that volume. In 3 mL of wholeblood, assume a total of 15 million white blood cells and 150 bacteria(50 per mL). The total DNA in this sample is approximately 90 μg, withessentially all of this due to leukocyte DNA. If this DNA were purifiedand recovered with 100% efficiency in a solution of 25 μL, the DNAconcentration would be 3.6 mg/mL, almost certainly inhibitory for PCR(F. B. Cogswell, C. E. Bantar, T. G. Hughes, Y. Gu, and M. T. Philipp(1996) “Host DNA can interfere with detection of Borrelia burgdorferi inskin biopsy specimens by PCR” J Clin Microbiology 34:980-982) and tooviscous for microfluidic manipulation. In contrast, the small amount ofbacterial DNA—only 250 genomes of approximately 5 Mbp/genome—present in25 μL would be approximately 1 pg. If only one-tenth of the total DNAwere to be used for the microfluidic reaction, the limit of detectionwould by definition decrease ten-fold. As blood volume increases, thenumber of leukocytes per unit blood volume increases, the microfluidicsolution volume decreases, and the number of organisms per sampledecrease, this problem becomes even more severe. The conclusion fromthis analysis is that in certain applications (particularly those inwhich bacterial load is low early in an infection), most of theleukocyte DNA should be removed before the final microfluidic volume isreached. This would allow most or all of the pathogen DNA to be analyzedfollowing purification. Similarly, background environmental DNA such asthat which accumulates on the filters of air breathers can interferewith the sensitivity and specificity of pathogen identification.

Removal of leukocytes in 3 mL of fresh human whole blood was achieved bystacking 13 layers of binding media with nominal pore size of 8 μm(Leukosorb B media, Pall Corporation, Port Washington, N.Y.) andfiltered using initial vacuum pressure of 0.25 psi and then wasincreased to 25 psi for final collection of filtrate. Useful pore sizesof binding media can range from less than 1 micron to over 100 microns,depending on the type of cells, virions, bacteria, fungi, andparticulates to be separated. Recovered volume was approximately 1.5 mLwith filtration completed in 1 minute. WBC counting of filtratesindicated that greater than 99% of leukocytes were retained by thefilter.

3 mL of fresh human whole blood samples were spiked with 100 μL of B.subtilis (ATCC® 7003™), with each 100 μL containing varyingconcentrations of B. subtilis per sample. In this experiment, B.subtilis was used as a model for pathogenic organisms and biothreatagents (e.g. B. anthracis). These blood-bacteria samples were passedthrough the stacked media using the apparatus of FIG. 1. Sampleapplication was followed by wash with 3 mL TSB (Tryptic Soy Brothmedia), allowing retrieval of bacteria that did not initially passthrough the binding matrix. Collected flow-through of approximately 4.5mL was passed through a single layer of 0.2 μm polycarbonate track-etchmembrane (SPI-Pore™ Track-Etch Membrane, Structure Probe, Inc., WestChester, Pa.) to concentrate the bacteria through capture on themembrane. This concentration method reduced reagent volumes, sizes ofthe purification cartridge reservoir chambers, and process time. Thecaptured organisms were collected from the surface of the membrane byresuspending in 100 μL PBS (Phosphate-buffered saline).

In this embodiment, the lysis of bacterial cells was based on chaotropicsalt extraction method for DNA and RNA. In particular, the preferredlysis buffer solution contained 4M guanidinium hydrochloride, 80 mMTris-HCI (pH 7.5), 20 mM EDTA and 5% Triton X-100 (other useful lysisbuffers are described in Ausubel et al., supra). To 100 μL ofresuspended organisms, 450 μL of lysis buffer with 1 mg/mL finalconcentration of proteinase K was transferred and mixed thoroughly inthe purification cartridge through the chaotic bubbling method definedin the pneumatic script. To this, 550 μL of absolute (200 proof) ethanolwas added and again mixed by bubbling. The lysate was passedmicrofluidically through a silica-based membrane for DNA binding in themicrofluidic portion of the purification apparatus. After the entirelysate was filtered, the membrane is washed with 2 mL of 1× washsolution prepared by mixing 1 unit volume of 200 mM NaCl solution, 0.5unit volume of 200 proof ethanol and 0.5 unit volume of >99%isopropanol. Following wash step, the membrane was then allowed to dryfor 1 minute by exposure to air from the pneumatic system. DNA wasfinally eluted in 20 μL TE buffer, pH 8.0. Pressures for lysatefiltration, membrane washing and drying, and elution were approximately5 psi. Fast PCR amplification (Giese, H. et al., (2009), “Fastmultiplexed polymerase chain reaction for conventional and microfluidicshort tandem repeat analysis” J Forensic Sci 54(6): 1287-97) using glnA(glutamine synthetase) primers in a microfluidic biochip and separatedand detected microfluidically results in the expected 343-bp fragmentcharacteristic of the B. subtilis glnA gene with signal intensityproportional to the input copies in blood samples. PCR was performedusing biochips and a fast thermal cycler as described in “Methods forRapid Multiplexed Amplification of Target Nucleotides,” PCT/US08/04487,which is hereby incorporated by reference. Separation and detection wereperformed on Genebench as described in “Plastic Microfluidic Separationand Detection Platforms,” PCT/US08/04405, and “Integrated Nucleic AcidAnalysis,” PCT/US08/04462, both of which are hereby incorporated byreference. FIG. 2 shows an electropherogram showing approximately 2genome equivalents of B. subtilis; this represents the amplification ofonly ˜6% of the total material recovered from a 33 cfu/mL blood sampleand using 40% of the PCR product for electrophoretic analysis. Bacterialrecovery is near-quantitative.

An alternative method for quantitation was to use a Petroff-Hausserchamber. Collected flow-through was plated on TSB-agar plates todetermine the effect of filtration through stacked media on the recoveryof bacteria. Recovered bacteria are normalized using plating efficiencybased on colonies recovered in unfiltered control samples. At clinicalrelevant concentrations of bacteria in blood, approximately 100% of thebacteria were recovered.

Expected Bacteria # of Colonies Recovered by % % Recovery in 3 mL ofBlood Plating Filtered Samples Recovery Normalized ~1000 860 ± 239 85 ±18 104 ± 10 ~100 88 ± 16 88 ± 11  97 ± 17 ~10 9 ± 2 96 ± 19 103 ± 26

FIG. 3 shows an integrated purification cartridge for blood samples.FIGS. 4, 5, and 6 show the macrofluidic component, pneumatic layer ofthe microfluidic component, microfluidic layer of the microfluidiccomponent, respectively, of the integrated purification cartridge. Themacrofluidic portion [3] of the apparatus is composed of 11 chambers,[6] to [16], that hold preloaded reagent solutions or serve asholding/reaction chambers during the DNA purification process. Onechamber is used to accept the blood collection tube; six chambers arepre-filled with 3 mL of wash buffer, 100 μL of resuspension solution,450 μL of lysis solution, 550 μL of absolute ethanol, 2 mL of washbuffer and 20 μL of TE (pH 8) elution buffer.

The apparatus accepts a standard 3 cc vacutainer tube (for separationexperiments, blood should be collected in tubes containing appropriateanticoagulants. The blood collection tube [1] is inserted into thecartridge with the rubber stoppered end down. The purification processis initiated when the user presses a start button. The apparatustogether with the instrument execute an automated script and generatepurified DNA. Within the instrument, the blood collection tube is pushedonto two hollow pins located at the base of blood collection tube cavity[16]. The hollow pins pierce through the rubber stopper to fluidicallyand pneumatically couple the blood collection tube to the apparatus. Theblood collection tube [16] is pressurized pneumatically to 5 psi todrive the blood from the blood collection tube [16] through theleukosorb filter [22] and track-etch membrane [21] to the waste chamber[8]. The filtrate that passes through the leukosorb filter contains thebiological material (e.g. bacterial, viral, or fungal pathogens) foranalysis, a leukocyte-reduced filtrate. This filtrate is then driventhrough a track-etch membrane, and the pathogens of interest areretained by the membrane (the pore size of the pathogen capture membraneis elected based on the dimensions of the pathogens to be analyzed).Wash solution from wash reservoir 2 [15] is pneumatically driven throughthe leukosorb filter [22] and track-etch membrane [21] to the wastechamber [8]. Resuspension solution from the resuspension solutionreservoir [4-10] is applied to the surface of the track-etch membrane[6-21]. This solution will resuspend the pathogens retained on the tracketch membrane, generating a concentrated pathogen suspension (which mayalso include residual leukocytes). This suspension is pneumaticallydriven into the lysis/waste chamber [11]. Lysis reagent is pneumaticallydriven into the lysis chamber [11]. Air is pneumatically driven into thelysis/waste chamber [11] to effect chaotic bubbling of the lysate withinthe lysis/waste chamber [11]. This bubbling creates flow of the lysateto mediate cell lysis. Ethanol from the ethanol reservoir [12] is driveninto the lysis/waste chamber [11]. Continued application of pneumaticdrive through the ethanol reservoir [12] after all the ethanol has beendispensed forces air through the lysate and ethanol solution to effectmixing by chaotic bubbling. All the lysate and ethanol mixture ispneumatically driven into the holding chamber [11]. From the holdingchamber [11] the lysate and ethanol mixture is pneumatically driventhrough the purification membrane [23] and into the lysis/waste chamber[11]. Wash solution from wash reservoir 1 [6] is pneumatically driventhrough the purification membrane [23] and into the lysis/waste chamber[11]. This wash removes unbound material and residual lysis solution.Continued application of pneumatic drive through the wash chamber [6]after all the wash solution has been dispensed will force air throughthe purification filter and dry the filter. Elution solution ispneumatically driven from the eluate reservoir [9] through thepurification membrane [6-23] to the eluate homogenization chamber [7].Continued application of pneumatic drive through the eluate reservoir[9] after all elution solution has been dispensed will force air througheluate homogenization chamber [7] to effect mixing by chaotic bubbling.Homogenized purified DNA solution in the eluate homogenization chamber[7] is ready for subsequent analysis.

Example II Intracellular Bacteria Present in Blood

Certain bacteria such as Francisella tularenis and Chlamydiatrachomastis spend a significant portion of their life cycles withinmammalian cells. Some are obligate intracellular organisms and othersare optionally intracellular. A comprehensive summary of known humanpathogens is provided by Gorbach, S. L. (et al. Eds.) Infectious Disease(3rd Ed), (2004 Lippincott Williams & Wilkins Pub). The DNA purificationprocess for such intracellular bacteria in blood is similar to that ofextracellular bacteria with a major exception. Following application ofwhole blood on and through the cell separation filter, the leukocytestrapped by the filter contain the DNA of interest. The filter is washed,resuspended in 100 μL, and subjected to guanidinium-based purificationas described in Example I with corresponding reduction is reagentvolume.

If desired, the apparatus can be design to initially lyse the leukocytes(osmotically, for example), taking advantage of the relative ease oflysis of mammalian cells as compared to bacteria. In this setting, theintact intracellular bacteria are released, and the cell extract isbased through a bacterial capture filter and washed. Bacterial DNA isthen purified as described in Example I. Similarly, whole blood can belysed in the absence of cell separation, allowing extracellular orintracellular bacterial or viral DNA to be purified.

Example III Purification of DNA from Biological Sample(s) Collected by aValidated Forensic Collection Swab

Forensic samples can be broadly divided into two types; casework samplesare those that are collected at a crime scene or in connection with aninvestigation, and reference samples are collected directly from anindividual. Several collection methods are available based on thespecific type of sample to be analyzed and are designed to obtain andprotect biological evidence from the crime scene. Swabbing is awell-established forensic sample collection method, and commerciallyavailable swabs have collection matrices consisting of various materialssuch as cotton, modified cellulose, foam, nylon, polyester and rayon.

FIG. 7 shows a purification cartridge for forensic swab samples. FIGS.8-10 show the macrofluidic component, pneumatic layer of themicrofluidic component, and the microfluidic layer of the microfluidiccomponent of the purification cartridge. The microfluidic portion [27]of the purification cartridge contains valves to control the flow of thesolutions to and from the macrofluidic portion [26], a particulatefilter [40], and a purification filter [41].

To purify DNA from a forensic swab sample, a BodeSecur swab was manuallyinserted into the sample collection chamber of the purificationcartridge and was locked into place for sample processing. The chamberthat accepts the swab was designed to allow the swab cap to fit snugly.The cartridge was designed to allow the operator to insert the swab intothe chamber and initiate DNA purification without further usermanipulation.

The macrofluidic portion of the purification cartridge was composed of 7chambers that hold preloaded reagent solutions or serve asholding/reaction chambers during the DNA purification process. Onechamber was used to hold the cotton swab with the DNA sample; fourchambers were pre-filled with 550 μL of lysis solution, 550 μL ofabsolute ethanol, 2 mL of wash buffer and 100 μL of TE (pH 8) elutionbuffer. The microfluidic portion of the purification cartridge containedvalves to control the flow of the solutions to and from the macrofluidicportion, a particulate filter, and a purification filter.

The sample collection swab (Bode SecurSwab) [24] is comprised of a cap,cotton swab head, and a shaft connecting the two; the total length ofthis sample collection device is approximately 9.1 cm. The swab head hasa nominal dimension of 5 mm to 5.1 mm in diameter and is approximately12 mm long. When the SecurSwab is inserted into the apparatus, the swabhead enters a tubular section of the sample chamber and is positionedbetween 0 mm to 1.5 mm from the bottom of the sample chamber. Thetubular section is 5.85 mm in diameter and 24 mm in length. An air inletport that is 1 mm in diameter is located at the bottom of the tubularsection. The diameter of the inlet port (between 0.1 mm and 2.5 mm andpreferably between 0.7 mm and 1.3 mm) and the dimensions of the tubularsection of the sample chamber can be modified to optimize fluid flow andchaotic bubbling.

The purification process was initiated by simply pressing a button thatstarts the automated script that controls the pneumatic drive. Thepneumatic drive applies the required pressures and vacuums for therequired times to enable all process steps to be conductedautomatically, without user intervention. Lysis solution waspneumatically driven from the lysis reagent reservoir [34] into the swabchamber [32] and brought in contact with the swab. Continued applicationof pneumatic drive through the lysis reservoir [34] after all the lysisreagent had been dispensed forced air through swab chamber effect“chaotic bubbling”. This was carried out, by the application of 5.7 psipressure for 60 seconds. This bubbling created turbulent flow around theswab head, mediating cell lysis and the removal of cellular materialfrom the swab head. Ethanol from the ethanol reservoir [33] was driveninto the swab chamber [32]. Continued application of pneumatic drivethrough the ethanol reservoir [32] after all the ethanol had beendispensed forced air through the lysate and ethanol solution to effectmixing by chaotic bubbling for 30 seconds. All of the lysate and ethanolmixture was pneumatically driven through a particulate filter [40] intothe holding chamber [35]. From the holding chamber [35] the lysate andethanol mixture was pneumatically driven through the purificationmembrane [41] and into the swab chamber [32]. The swab chamber nowserved as a waste chamber for spent process reagents. Wash solution fromwash reservoir [29] was pneumatically driven through the purificationmembrane [41] and into the swab chamber [32]. Washing of thepurification membrane with wash buffer was conducted to remove unboundmaterial (including protein) and residual lysis solution. Continuedapplication of pneumatic drive through the wash reservoir [29] after allthe wash solution had been dispensed forced air through the purificationfilter [41] and dried the filter for 105 seconds. Elution solution waspneumatically driven from the eluate reservoir [31] through thepurification membrane [41] to the eluate homogenization chamber [30].Continued application of pneumatic drive through the eluate reservoir[31] after all elution solution had been dispensed forced air througheluate homogenization chamber [30] to effect mixing by chaotic bubbling.Homogenized purified DNA solution in the eluate homogenization chamber[30] was ready for subsequent analysis.

To evaluate the DNA generated by the purification cartridge, rapidmultiplex PCR reactions were performed as described in Geise et al. 2009(supra) using AmpFlSTR® Identifiler® primers (Life Technologies) in avolume of 7 μL in approximately 17 minutes. Amplified products wereseparated and detected using NetBio's Genebench. To 2.7 μL of eachamplified product 10.2 μL Hi-Di formamide and 0.1 μL of Genescan 500 LIZinternal lane standard (both Life Technologies) were added. Afterdenaturation at 95° C. for 3 min and snap cooling on ice, samples wereloaded into the wells of the separation biochip and electrophoreticallymoved into the separation channels by applying a 350 V/cm electric fieldfor 90 seconds. This was followed by the application of a 150 V/cmelectric field along the separation channel to separate the DNAfragments. All separations were carried out at 50° C. Raw data wereanalyzed with the GeneMarker® HID STR Human Identification Software,Version 1.51 (SoftGenetics LLC, State College, Pa.).

Full allelic profiles from various swab samples (buccal swabs, dried andwet whole blood in swabs, saliva and cellular touch) were generated.Buccal cell samples (FIG. 11) are obtained by lightly scraping the swabson the inside cheek of a human subject. Dried blood sample are preparedby swabbing dried bloodstains (FIG. 12). Saliva samples (FIG. 13) arecollected by swabbing saliva present on a ceramic tile. Touch samples(FIG. 14) are prepared by swabbing a ceramic tile that was handled by asingle donor. The swab head was pre-wet with sterile DI water.

Example IV Bacterial DNA from a Vaginal Swab

A vaginal swab is inserted into the purification cartridge samplechamber through a clamping port to hold the swab in place. Thepurification is essentially the same as that described for forensicswabs in Example III; the main difference is that the sample chamber ismodified to accept and secure the vaginal swab. The geometry of the swabchamber can be modified to accommodate essentially any swab type,regardless of the dimensions of the swab handle or collection region ofthe swab. The sample chamber is designed such that the swab can bedirectly inserted into the purification cartridge for processing. Thecap of the swab may be modified to lock irreversibly to minimize thepossibility of sample-to-sample contamination, and the swab assembly maybe modified to allow sample identification (e.g. by bar-code or RFIDchip).

FIG. 15 shows a purification cartridge for vaginal or cervical swabsamples and FIG. 16 shows the macrofluidic portion of that cartridge.The microfluidic layers are essentially the same as those of FIGS. 9 and10.

The macrofluidic portion of the purification cartridge is composed of 7chambers that hold preloaded reagent solutions or serve asholding/reaction chambers during the DNA purification process. Onechamber is used to hold the cotton swab with the DNA sample; fourchambers are pre-filled with 550 μL of lysis solution, 550 μL ofabsolute ethanol, 2 mL of wash buffer and 100 μL of TE (pH 8) elutionbuffer.

The purification process is initiated by simply pressing a button thatstarts the automated script that controls the pneumatic drive. Thepneumatic drive applies the required pressures and vacuums for therequired times to enable all process steps to be conductedautomatically, without user intervention. Lysis solution ispneumatically driven from the lysis reagent reservoir [52] into the swabchamber [50] and brought in contact with the swab. Continued applicationof pneumatic drive through the lysis reservoir [52] after all lysisreagent has been dispensed will force air through swab chamber effect“chaotic bubbling” at 5 psi for 60 seconds. This bubbling createsturbulent flow around the swab head, mediating cell lysis and theremoval of cellular material from the swab head. Ethanol from theethanol reservoir [51] is driven into the swab chamber [50]. Continuedapplication of pneumatic drive through the ethanol reservoir [51] afterall the ethanol has been dispensed will force air through the lysate andethanol solution to effect mixing by chaotic bubbling for 30 seconds.All the lysate and ethanol mixture is pneumatically driven through aparticulate filter [40] into the holding chamber [35]. From the holdingchamber [35] the lysate and ethanol mixture is pneumatically driventhrough the purification membrane and into the swab chamber [50]. Theswab chamber now serves as a waste chamber for spent process reagents.Wash solution from wash reservoir [47] is pneumatically driven throughthe purification membrane and into the swab chamber [50]. Washing of thepurification membrane with wash buffer is conducted to remove unboundmaterial (including protein) and residual lysis solution. Continuedapplication of pneumatic drive through the wash reservoir [47] after allthe wash solution has been dispensed will force air through thepurification filter and dry the filter for 105 seconds. Elution solutionis pneumatically driven from the eluate reservoir [49] through thepurification membrane to the eluate homogenization chamber [48].Continued application of pneumatic drive through the eluate reservoir[49] after all elution solution has been dispensed will force airthrough eluate homogenization chamber [48] to effect mixing by chaoticbubbling. Homogenized purified DNA solution in the eluate homogenizationchamber [48] is ready for subsequent analysis.

Total nucleic acid concentration is quantified by absorbance at 260 nm.Fast PCR amplification in biochip using fluorescently-labeled primersets specific for sexually transmitted diseases (including Chylamdiatrachomatis, human immunodeficiency virus, Trichomonas vaginalis,Neisseria gonorrhoeae) and electrophoretic separation and detection inGenebench generate bands characteristic of the pathogen causing eithersymptomatic or asymptomatic infection.

While these inventions have been particularly shown and described withreferences to preferred embodiments thereof, it will be understood bythose skilled in the art that various changes in the form and detailsmay be made therein without departing from the spirit and scope of theinventions, as described in the appended claims.

1. A self-contained apparatus for isolating nucleic acid from anunprocessed sample, said apparatus to be used with an instrument, saidapparatus comprising at least one input, and: (i) a macrofluidiccomponent, comprising a chamber for receiving said unprocessed samplefrom a collection device and at least one filled liquid purificationreagent storage reservoir; (ii) a microfluidic component incommunication with said macrofluidic component via at least onemicrofluidic element, said microfluidic component further comprising atleast one nucleic acid purification matrix; and (iii) a drive mechanismon said instrument for driving said liquid purification reagent, throughsaid microfluidic element and said nucleic acid purification matrix,wherein the only inputs to said apparatus are via said chamber and saiddrive mechanism.
 2. The apparatus of claim 1 wherein said collectiondevices and/or chambers are labeled, said labels comprising a bar codeor RFID.
 3. The apparatus of claim 1 wherein said drive mechanism ispneumatic, mechanical, magnetic, or fluidic.
 4. The apparatus of claim 1wherein the unprocessed sample comprises: i) a nasal swab,nasopharyngeal swab, buccal swab, oral fluid swab, stool swab, tonsilswab, vaginal swab, cervical swab, blood swab, wound swab, or tubecontaining blood, sputum, purulent material, or aspirates; (ii) aforensic swab, cutting, adhesive tape lift, or card; or (iii) anenvironmental air filter, water filter, or swab.
 5. The apparatus ofclaim 1 wherein the nucleic acid purification matrix comprises silicamembranes, silica beads, silica magnetic beads, ion exchange resins, orion exchange beads.
 6. The apparatus of claim 1 wherein saidmicrofluidic component comprises channels, reservoirs, active valves,passive valves, pneumatically actuated valves, reaction chambers, mixingchambers, venting elements, access holes, pumps, metering elements,mixing elements, heating elements, magnetic elements, reaction chambers,filtration elements, purification elements, drive lines, or actuationlines.
 7. A method for purifying nucleic acids from an unprocessedsample comprising, providing a sample comprising nucleic acids to thechamber of an apparatus of claim 1; driving at least a portion of afirst lysis reagent from said first lysis reagent chamber into thechamber to provide a first mixture; driving at least a portion of asecond lysis reagent from said second lysis reagent chamber into thechamber to provide a second mixture; driving at least a portion of thesaid second mixture through the purification membrane to provide afiltrate and a retentate, wherein the retentate comprises at least aportion of the nucleic acids; driving at least a portion of the washreagent through the purification membrane to provide a washed retentateand a waste; optionally drying the washed retentate; and collecting atleast a portion of the nucleic acids from the washed retentate bydriving at least a portion of an elution reagent from the elutionreagent chamber through the purification matrix.
 8. The method of claim7, wherein the unprocessed sample comprises: (i) a nasal swab,nasopharyngeal swab, buccal swab, oral fluid swab, stool swab, tonsilswab, vaginal swab, cervical swab, blood swab, wound swab, or tubecontaining blood, sputum, purulent material, or aspirates; (ii) aforensic swab, cutting, adhesive tape lift, or card; or (iii) anenvironmental air filter, water filter, or swab.
 9. A method forpurifying nucleic acids from pathogens in whole blood comprising,providing a sample comprising anticoagulated whole blood and pathogensin a blood collection tube to the sample collection chamber of anapparatus of claim 1; driving at least a portion of the blood through aleukocyte retention filter to provide a reduced-leukocyte filtrate;driving at least a portion of a leukocyte wash reagent through theleukocyte retention filter to provide a washed reduced-leukocytefiltrate; driving at least a portion of the a reduced-leukocyte filtratethrough a pathogen capture membrane driving at least a portion of thepathogen resuspension solution across the capture membrane to provide aconcentrated pathogen suspension driving at least a portion of theconcentrated pathogen suspension into a first lysis reagent chambercontaining said first lysis reagent to provide a first mixture; drivingat least a portion of a second lysis reagent from said second lysisreagent chamber into the first lysate reagent chamber to provide asecond mixture; driving at least a portion of the said second mixturethrough the purification membrane to provide a filtrate and a retentate,wherein the retentate comprises at least a portion of the nucleic acids;driving at least a portion of the wash reagent through the purificationmembrane to provide a washed retentate and a waste; optionally dryingthe washed retentate; and collecting at least a portion of the nucleicacids from the washed retentate by driving at least a portion of anelution reagent from the elution reagent chamber through thepurification matrix.
 10. A method for purifying nucleic acids frompathogens in whole blood comprising, providing a sample comprisinganticoagulated whole blood and pathogens in a blood collection tube tothe sample collection chamber of an apparatus of claim 1; driving atleast a portion of the blood through a leukocyte retention filter toprovide a reduced-leukocyte filtrate; driving at least a portion of aleukocyte wash reagent through the leukocyte retention filter to providea washed reduced-leukocyte filtrate; driving at least a portion of theleukocyte resuspension solution across the retention filter to provide aconcentrated leukocyte suspension driving at least a portion of theconcentrated leukocyte suspension into a first lysis reagent chambercontaining said first lysis reagent to provide a first mixture; drivingat least a portion of a second lysis reagent from said second lysisreagent chamber into the first lysate reagent chamber to provide asecond mixture; driving at least a portion of the said second mixturethrough the purification membrane to provide a filtrate and a retentate,wherein the retentate comprises at least a portion of the nucleic acids;driving at least a portion of the wash reagent through the purificationmembrane to provide a washed retentate; optionally drying the washedretentate; and collecting at least a portion of the nucleic acids fromthe washed retentate by driving at least a portion of an elution reagentfrom the elution reagent chamber through the purification matrix. 11.The method of claim 10, said method additionally comprising, driving aleukocyte lysis solution into the concentrated leukocyte suspension toprovide a differentially lysed suspension driving at least a portion ofthe differentially lysed suspension through a pathogen retention filterdriving at least a portion of the retention filter wash reagent throughthe pathogen retention filter to provide a washed pathogen retentate;and resuspending, lysing, and purifying nucleic acids from the pathogenretentate as in claim
 10. 12. A self-contained apparatus for generatingcell lysate from an unprocessed sample, said apparatus to be used withan instrument, said apparatus comprising at least one input, and: (i) amacrofluidic component, comprising: a chamber for receiving saidunprocessed sample from a collection device, and at least one filledreagent storage reservoir; and (ii) a microfluidic component incommunication with said macrofluidic component via at least onemicrofluidic element; and (iii) a drive mechanism on said instrument fordriving said reagent, through said microfluidic element, wherein theonly inputs to said apparatus are via said chamber and said drivemechanism.
 13. The apparatus of claim 12, wherein the reagent comprisesa lysis reagent.
 14. A self-contained apparatus for lysing cells from anunprocessed sample, said apparatus to be used with an instrument, saidapparatus comprising at least one input, and: (i) a macrofluidiccomponent, comprising a chamber for receiving said unprocessed samplefrom a collection device and at least one pre-filled lysis storagereservoir; and (ii) a microfluidic component in communication with saidmacrofluidic component via at least one microfluidic element; and (iii)a drive mechanism on said instrument for driving reagent in said storagereservoir, through said microfluidic element; wherein the only inputs tosaid apparatus are via said chamber and said drive mechanism.
 15. Amethod for lysing cells from a sample comprising using the apparatus ofclaim 14, comprising: providing a sample comprising cells to a chamber;introducing said lysis reagent into the chamber to provide a mixture;bubbling a gas through the mixture to provide a stirred mixture; whereinthe stirred mixture comprises lysed cells.
 16. A self-containedapparatus for generating a suspension of cells from an unprocessedsample, said apparatus to be used with an instrument, said apparatuscomprising at least one input, and: (i) a macrofluidic component,comprising: a chamber for receiving said unprocessed sample from acollection device, and at least one filled reagent storage reservoirstoring a substantially isotonic reagent; and (ii) a microfluidiccomponent in communication with said macrofluidic component via at leastone microfluidic element; and (iii) a drive mechanism on said instrumentfor driving said reagent, through said microfluidic element; wherein theonly inputs to said apparatus are via said chamber and said drivemechanism.
 17. The apparatus of claim 1, wherein the instrument alsoperforms at least one of thermal cycling, capillary electrophoresis,microfluidic electrophoresis, nucleic acid fragment sizing, short tandemrepeat (STR), Y-STR, and mini-STR, single nucleotide polymorphism, PCR,highly multiplexed PCR, Real-time-PCR, Reverse Transcription PCR,sequencing, hybridization, microarray, VNTR, immunoassays, massspectroscopy and RFLP analyses.
 18. The apparatus of claim 1, whereinthe apparatus can be placed into or interfaces with another instrumentthat performs at least one of thermal cycling, capillaryelectrophoresis, microfluidic electrophoresis, nucleic acid fragmentsizing, short tandem repeat (STR), Y-STR, and mini-STR, singlenucleotide polymorphism, PCR, highly multiplexed PCR, Real-time-PCR,Reverse Transcription PCR, sequencing, hybridization, microarray, VNTR,immunoassays, mass spectroscopy and RFLP analyses.
 19. The apparatus ofclaim 17, wherein the apparatus and instrument are ruggedized towithstand transport and extremes of at least one of temperature,humidity, and airborne particulates.